Table 1.
Available software for signatures of selection analysis.
| Software | Analysis | Availability | References |
|---|---|---|---|
| PLINK v1.07 and v1.90beta | Quality control, data management, cryptic relatedness check, and computation of runs of homozygosity and FST | http://pngu.mgh.harvard.edu/~purcell/plink/ | Purcell et al., 2007 |
| https://www.cog-genomics.org/plink2 | |||
| SNP & Variation Suite v7.6.8 | Quality control, data management, cryptic relatedness check, and computation of runs of homozygosity and FST | http://www.goldenhelix.com | Golden Helix, Bozeman, MT, USA |
| GCTA v1.24.2 | Quality control, data management, and cryptic relatedness check | http://www.complextraitgenomics.com/software/gcta/ | Yang et al., 2011 |
| fastPHASE v1.2 | Phasing and imputation of missing genotypes | http://stephenslab.uchicago.edu/software.html#fastphase) | Scheet and Stephens, 2006 |
| Beagle v3.3 and v4.0 | Phasing and imputation of missing genotypes | http://faculty.washington.edu/browning/beagle/beagle.html | Browning and Browning, 2008 |
| SHAPEIT2 | Phasing and imputation of missing genotypes | https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html | O'Connell et al., 2014 |
| Sweep | EHH-based methods | http://www.broadinstitute.org/mpg/sweep/ | Sabeti et al., 2002 |
| selscan | EHH-based methods | https://github.com/szpiech/selscan | Szpiech and Hernandez, 2014 |
| rehh | EHH-based methods | http://cran.r-project.org/web/packages/rehh/index.html | Gautier and Vitalis, 2012 |
| FLK | Computation of the FLK statistics | https://qgsp.jouy.inra.fr/index.php?option=com_content&view=article&id=50&Itemid=55 | Bonhomme et al., 2010; Fariello et al., 2013 |
| SweepFinder | Computation of the CLR statistics | http://people.binf.ku.dk/rasmus/webpage/sf.html | Nielsen et al., 2005 |
| XP-CLR v1.0 | Computation of the XPCLR statistics | http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html | Chen et al., 2010 |
| cosi and cosi2 | Coalescent simulations | http://www.broadinstitute.org/~sfs/cosi/ | Schaffner et al., 2005; Shlyakhter et al., 2014 |
| http://www.broadinstitute.org/~ilya/cosi2/ | |||
| MSMS | Coalescent simulations | http://www.mabs.at/ewing/msms/index.shtml | Ewing and Hermisson, 2010 |